You're My Father?
by kcms123
Summary: Clary doesn't got out and is home when Jocelyn is attacked. She never met Jace, but instead her Dark Prince and her real Father. The Mortal Instruments belong to Cassandra Clare. I own nothing but the plot of this fanfic.
1. Chapter 1

**You're My Father?**

 **This is my first time so be nice...**

* * *

"Mum it's my birthday and I would like to go out with Simon, it's not that big a deal, we are just going to Java Jones to listen to Eric's lousy poetry." Clary stood facing the mirror in her bedroom, practicing her argument. She really needed to leave this apartment, her Mothers been particularly strict lately and Clary hasn't been allowed to go anywhere. She watched herself take a deep breath, before turning and walking calmly to the lounge room. Clary takes another deep breath as she turns the corner, she spies her Mother painting something beautiful in deep concentration.

"Mum?"

"Uh?"

"Mum it's my birthday and I would like to go out with Sim-"

"NO!" Jocelyn shouts, dropping her paint brush to the floor. Clary jumps back in surprise, and gave her mother a dirty look, she knew there was a high chance that the answer was going to be no but she didn't even get to finish her argument.

"Come on please, it's not that big a deal, we are just going to go to Java Jones to listen to Eric's lousy poetry."

"No Clary, at that's my final answer." Jocelyn rubbed her temple in an attempt calm down, "I'm sorry but one of the buyers of my paintings is coming by later and I really need you to be here."

 _Well at least I finished my argument…_ Clary sighed and turned to leave, saying over her shoulder,

"I guess I'll shower for your mysterious buyer."

Clary turned into the bathroom, kicking the door shut before her overly strict Mother could respond. She wasn't really in any state to be seen in public anyway, she decided after looking in the mirror, noticing the mess of hair and crappy clothing. She sighed again turn on the water and stripping down and stepping under its soothing stream, not hearing anything but the water hitting her head.

* * *

Jocelyn sigh, drumming her fingers on the ground as she cleaned up the paint, she would do whatever she could to protect her daughter even if that means making an enemy of herself. Three knocks at the door interrupted her thoughts, Jocelyn frowned as she stood, Magnus wasn't supposed to be here for another 2hrs. Jocelyn silently went to the door and peered through the hole. She jumped back quickly barely avoiding contact by the flying door as a shadow hunter charges through the door wearing long black cloak, with his hood pushed back. Jocelyn bolted to the kitchen slamming the door closed behind her and grabbing the potion. She fumbled with the box, why she decided to put it in such an elegant, hard to open box, was beyond her.

"Jocelyn?" Was called out to her sweetly in a sing-song manner. Jocelyn pause, her eyes widened in horror, "Where's the cup?"

"No…" She whisper, quietly to herself as she finally pried open the box. "You are never going to get it." She screams loudly. Pieces of wood flew at her as a fist slammed through the door. She yanked out the poison after finally popping the lid.

"Come on, sweet heart, open the door."

"VALENTINE LEAVE ME ALONE!" She screamed, before swallowing the poison.

"MUM?"

Jocelyn froze in horror, before looking down at the bottle in her hand,

"No, no, no, no…oh no…" She could feel her heart rate accelerating, her head pounding and her vision blurring as the poison went to work. The door exploded open just as she felt herself falling to the ground,

"Run Clary, RUN!" She tried shouting, but she could barely hear it, having it been only just louder than a whisper.

* * *

Jonathan paused at the broken doorway, admiring the mess of the apartment before carefully making his way through to his Father in the kitchen, just catching the nasty back-hand he gives to Blackwell.

"YOU WEAK, WORTHLESS PIECE OF SHIT! Look at what happened because YOU couldn't open a damn door." Valentine screamed. Jonathan smiles he's always hated that moron, and his blinding loyalty to Father.

"I apologies, my lord." He whimpers from the floor, head bowed at Valentine feet.

"Just get up and go look for the cup."

"MUM, WHAT GOING ON? ARE YOU OK?" A voice calls from another room, Jonathan forces a blank face, and doesn't move, like the good little solider he is. Even though he is dying to find the source of that beautiful voice. He waits patiently as his Father to order him to do so.

"Go." He says shortly, but it's all he need. Jonathan forces himself to slow down and not outright sprint when he hears flowing water. He reaches the door to what he assumes is the bathroom and unsurprisingly fails to turn the handle, as he reaches for his stele, as the shower turns off. As apartment is already a mess he decided to just charge right in. The door explodes under his weight, wood flying everywhere, but that didn't hurt nearly as much as his dick in his pants when he sees her naked form, pale skin with red almost everywhere he looks, red hair, red checks, pink nipples and beautiful short, red curls. He didn't hear the scream from her lips, but he did see her large, pink lips part as she did so, she grabs a towel and quickly covered herself. Once she had the towel secure around her small frame, Jonathan had quickly schooled his features and controlled his breathing so no-one knew just how much he wanted to rip that towel from her grasp. She stared at him wide eyed, and he stared right back. She glanced to his right and attempt to run past him. Jonathan quickly wraps his arm her narrow waist, bringing her close to his chest, appreciating how it force the towel to ride up revealing more of her short, pale legs. Clary fights his tight hold in a pitiful attempt to break free, but he merely picks her up and holds her across his chest.

"Be still," Jonathan whispers softly in her ear as he began carrying her to the lounge room, to his absolute amazement she does, she relax in his hold, to which he response by slightly loosening his grip and appreciating the soft skin of her thighs and arm against his hands as he carries her to the destroyed lounge room.

* * *

Clary was in shock, her apartment appears to have been destroyed in the ten minutes that she was in the shower, she had been thinking about Simon, her Mum and breaking out and must have been very deep in her own head to not have heard any of it. And now she was in the arms a strange boy who has seen her naked and looks scarily like her Dark Prince. In the back of her head she knew that she should be fighting him, but she wasn't, both because she knew she could never win and because she somehow feels like she can trust him, like she's know him her whole life.

"MUM!" Clary gasps, covering her mouth as she sees her Mothers limb form, she once again begins fighting her Dark Princes hold, he gently put her on the opposite couch he gives her a hard look, which silently tells her not to move, and Clary was once again in shock. She swallows deeply and looks around the room avoid her Mothers still form and her Dark Princes eyes, noticing three other men in the room, two dress in black, one of which has a nasty red mark on his face, and another man simply wearing jeans and a plain blue T-shirt. Her eyes hurt when she looked at him for too long, so she ignored him and focused her attention on the white-blond, tall, dark eyed man who was smiling sweetly in the middle. Clary holds the towel to her chest tightly as she stares angrily at the man who dare hurt her mother. He takes a few steps towards her and get down on one knee in front of her. He tilts his head slightly to one side as he studied her.

"Hello, my dear. My name is Valentine Morgenstern." He stated sweetly, extending a hand to her. Clary glanced over at her Mother, before turning back to him. She squinted her eyes at him, "And you are?" he asks eyebrows raised in question.

"Clary." She utters softly, gripping her towel tightly. He lowers his hand and smiles before asking,

"Full name, please." She was curious as to why he was being nice, people were so much easier to be angry at when they were being mean and nasty.

"Clarissa Adele Fray," she stated firmly, some of the shock wearing off, and curiosity and anger setting in. Valentine nods without taking his eyes off her, he notices some fire in her eyes, and his eyebrows twitch together.

"You don't look like Lucian." He states almost in a confused like manner. Clary looks up at this in equal confusion, eyes dulling slightly at the name of her mum's friend.

"Why would I look like Luke?" Valentine's nose scrunches in disgust he stands,

"Is he not your Father? I would have assumed Jocelyn ran off to be with that beast."

Clary stood up at this almost hitting the rock hard muscles of the man in front of her, "LUKE IS NOT A BEAST", she exclaimed angrily, then after registering what she had done and the look outrage in the large man's eyes. She quickly sat back down and continued in a slightly softer tone, "and he's not my Father either, although he has pretty much raised me." Clary glances to the picture of her Father on the mantle above the fire, before casting her eyes down, hoping to avoid the anger in the large man's eyes through submission.

"Then who is your biological Father?" Valentine inquires, softly curious. Clary looks up and nods her head to the picture,

"His name is Jonathan, he died before I was born… Mum morns his death every year." Clary answers softly, watching Valentine walk to the picture, admiring it for a moment before returning to her, eyebrows furrowed.

"How old are you?" Valentine inquires in a soft tone.

"Sixteen" Clary replies at an almost whisper, she looks up and catches the look of shock that crosses everyone's face when she tells them how old she is, she looks twelve. Sighing she glances up at the picture of her Father, glad it wasn't destroyed, before flicking her eyes to her mother still form.

"Impossible…" She barely heard Valentine murmur.

"No, I can assure you I am, I know I don't look it but I am." Clary response angrily, _why does no-one believe her_? Valentine looks at her again for a moment.

"I do not believe that the man in this picture is your Father, it is impossible." He states after a few moments. Clary's eyebrows jump at this,

"Oh, and what makes you say that?"

"Because, my sweet child, your mother was married to me sixteen years ago… Still is in fact," He states, staring at her with a small smile on his face.

"So, what you're trying to say is, you…" She says pointing at him, swirling her finger a bit, "You are my Father?" He smiles broadly,

"Yes, Clarissa, I believe I am." He states happily, before scrunching his nose slightly and staring at the wall behind her in thought, "Clarissa's not a name I would have picked." He states looking back at her.

"Well that's nice, because my name is Clary." She says calmly, hoping to get the message across, she hated being called by her full name. Valentine laughs before turning to the man in the blue shirt,

"Warlock, ready the portal." He orders still staring at her. She saw Warlock nod in the corner of her eye, only for a second he appeared all blue, she blinked and looked again and he was back to normal, and so she forgot about it. Then Valentine turned to her Dark Prince, who had not stopped staring at her, eyes brows slightly furrowed when Valentine claimed to be her Father.

"Jonathan, take Clarissa to her room so she can get dressed." … _Jonathan, that's her Dark Princes name, weird that it's the same as her supposed father, I guess it was fairly common…_ Clary thought before registering the rest of the comment.

"Clary…my name is Clary." She stated, still half in her own head, but as soon as Jonathan came closer to her and moved to pick her up again, she snapped out of it, and stood up quickly. Once again almost hitting the rock hard muscles of the man in front of her, only this time a part of her wanted to touch the muscles. Clary felt the heat of a blush spread across her face as she looked up into Jonathan's face, his lips twitched a little before he stepped back and allowed her to pass into the hall. Clary quickly walked to her room, holding her towel tightly as she walked. She made it to her room in record time and turned to close the door be her Dark Pri- Jonathan could make it in. She wasn't nearly fast enough, and Jonathan was past her in a flash, casually admiring the drawing all over her room. She turned red when she spied her Dark Prince on her wall, silently comparing their differences, there weren't many.

"You're very good." He stated, in his soft, silky voice. She noticed him staring at her Dark Prince too, hopefully he won't think it's him, because that could be awkward.

"Thanks." She's whispers softly, looking down as he turned his hot, heavy gaze onto her. She swallowed,

"I better get dressed." She stated and moving out of the doorway.

"Go ahead." He states smiling, moving back to sit on her bed, still staring at her.

"So you're not going to leave, while I change?" She asking clutching her towel as she felt herself get warm all over.

"Nope." He states, leaning back a little not breaking eye contact.

"Such a gentleman." She murmurs sarcastically, while shutting the door. She could do this, she got changed around Simon all the time, although at least he had the decency to turn around. She wanders over to her wardrobe, grabbing underwear, bra, a simple t shirt, some jeans and a jacket. When she turned back Jonathan had really made himself at home on her bed, with his head perched on two pillows and his arm, his booted feet crossed at the ankles and the ever present smirk on his face.

"Ready for the show?" She asks sarcastically while dumping her clothes on the bed next to his feet.

"Absolutely," Clary's face felt so hot from her blush, though she tried to look unaffected by his confidence. Getting dressed around the towel went well once she turned her bad to him and stopped fumbling. When she was done she turned back around to find him looking dazed, smirks gone from his face. She blushes further when she notices the large bulge in his pants,

"You are such a pervert." A small smile once again touches his lips, but before he could reply, her phone began to ring. They both freeze for a moment and stare at the ringing phone, before Clary glances at Jonathan and pounces for it. He moves lightning fast, jumping from the bed, grabbing it and holding it loosely in his hands, face blank of any emotions. Clary reaches for it, but he simply holds it up above his head. _I will not jump for it, I will not jump for it_ , she chants in her head. The ringing stops and Clary stares at the phone, strategizing ways to get it, when it starts ringing again. She immediately jumps up, arm outstretched high, fingers barely grazing his wrist. She stops and crosses her arms across her chest and give the boy in front before her, her evilest glare. Watching the smirk grow bigger on his face. She huffs out excess CO2, before turning and walking back into the lounge room.

"Portals done, my lord." Warlock exclaims happily.

"What?" Clary questions. "Portal, like portal, portal? Like teleportation?" Clary asks in slight awe, looking around for it.

"Yes, well, it's a five-dimensional door," Valentine answered, "Dimensions aren't straight lines, you know," he added, in response to Clary's blank look. "There are dips and folds and nooks and crannies all tucked away. It's a bit hard to explain when you've never studied dimensional theory, but, yes it will take you anywhere in this dimension that you want to go." Valentine explained, pointing at the wall. When Clary focused on it she did notices it wobble and wave slightly, and that was enough for her, she pounced through. She was picturing Luke's bookshop, its old wood and smell, when she felt a tight grip on her ankle. In the momentary distraction she felt herself get pulled and stretched, so she doubled her efforts on picturing Luke's shop. Eye's closed in deep concentration until she hit the concrete hard.


	2. Chapter 2

"Clary rolls over, sucking the air back into her lungs, squinting up at the sun in a daze. She was contemplating sitting up when a bag of blond, muscles lands on top of her. Their forehead banging together, her knees slamming against someone else's. Tangled up in arms and legs, Clary opens her mouth to scream but instead gets a mouth full of hair. She tries to struggle out from under the crushing weight on top of her when it suddenly disappears. She sits up and see's Jonathan standing a few feet away, arms crossed over his chest with an angry scowl on his face.

"And just what do you think you are doing?" He calmly asks, one eyebrow raised slightly in question. Making Clary instantly jealous and angry, she'd always wanted to do that.

"Escaping." She responds simply, before turning and walking toward Luke's house. She takes approximately two and a half steps before being yanked by the arm, dragged to an alley and slammed against the wall.

"You wanted to escape from your own home, your own family?" He asks, as though astounded by the thought, but she got the feeling that he understood completely like he had previously considered the same. Even if her mother wasn't unconscious and her house wasn't destroyed, he would still understand her wanting to pounce at a wall that was once solid to escape a man claiming to be her Father. So she just stared at him, letting him realise that she wouldn't answer stupid questions while pinned to a rough wall. He shook his head and released her,

"Where are we anyway?" He asked sighing.

"Luke's house." She explained breaking eye contact and peering behind him to the bookshop, weighing her options. Jonathan turns slightly to look, still standing close enough to touch. His eyebrows scrunched, before meeting her eyes again.

"He lives in a bookshop?"

"Yeah, well sort or, he lives behind the book shop. Come on let's go meet him." She answers, smiling sweetly, before shoving past him and back onto the footpath.

"I don't think so." He whispers in her ear, sending goose bumps through her body. He hooks his arm through hers and turns her away from the safety of Luke's home. Well, it was worth a try…

They had been walking for a while, and naturally, Clary was lost in her own head, visualising probable escape paths, when she was rudely interrupted from her thoughts by an annoying, hypnotising, beautyfu- ugly voice.

"Stop trying to think of ways to escape. One: you would never get past me, and two: we are currently being tracked and Valentine will be here any moment to take us home." He explained simply, as though reading her thought. She squints up at him, wondering if he can… ugly, annoying, asshole, kittens, puppies, sex, penis, surfing, books, dogs surfing, cats playing the piano, muscular abs, naked Jonathan … He glances down at her,

"What?" He questioned curiously,

"Nothing." She responded quickly, heat spreading through her cheeks, turning away she notices the gorgeous buildings around her, one painted teal. She decided that today that was her favourite colour. She was still considering the difference between teal and turquoise when Jonathan stops and tugs her into an ice-cream shop. She glances up at him in confusion, sensing her gaze, he turns to her with what appears to be, an attempted look of innocence.

"What? I felt like ice-cream. I assume you want something?" He questions.

"Ah, yeah, sure, um… Chocolate, please." He turns to a flushed waitress, who immediately leans forward, propping her arm under the breasts so her cleavage is more prominent, and flutters her eyelashes. Clary feels a wave a jealousy coursed through her, she had no right to be jealous they had just met that day, it wasn't like they were getting married or anything. What if she didn't like the way he ate. She clenches her teeth and looks away as Jonathan smirks, sexily at the waitress.

"I would like two chocolate ice-creams in a cup, please." He asks, eyes peering, deeply into hers. Clary scrunches her nose in disgust, I don't care what people think, I am definitely attracted to him, and I am going to win his heart, she smiles evilly with a clever plan forming in her mind. She was going to attempt... flirting.

* * *

Jonathan watches the nice lady behind the counter intently, as she scoops some ice-cream into a cup and places it in on the counter in front of Clary, never once breaking eye contact with him. She then scoops some more into a cup for him, she glances at his mouth and smiles sweetly as she passes over his ice cream. He very carefully skims the tips of his fingers over her hand as he takes his ice-cream and watches her melt at his touch.

"Thank you." He murmurs, noticing his sister expression, and mentally pats himself on the back. He was going to make her love him, he needed her to be his, he needed someone who loved him. He just hoped that when she found out that they were related it wouldn't change her feelings. He avoided eye contact with his sister as they made their way to a table and sat, knowing it would drive her crazy. He glances up as they sit down, hoping to catch a good reaction, but all he gets is a small smile, though he is pleased to also catch a dark look in her eye. Not nearly as dark as he was sure his eyes got sometimes. But it did reinforce the idea that she was perfect for him, his sister, his blood. He feels himself smile slightly at the mere idea.

Without breaking eye contact with him, she scoops a small amount of ice-cream onto her spoon, before flipping over onto her outstretched tongue and slowly sliding the spoon into her mouth. The spoon had all but disappeared, when she sighs and closes her eyes, slowly pulls the spoon halfway out, before plucking her lips around its small handle and pushing it back in, groaning. Jonathan swallowed deeply, eyes wide, he usually felt as though he was prepared for any situation. But he did not see this coming. He knew Clary needed a distraction and he wanted to get to know his little sister. When he saw the ice-cream store he thought it would be the perfect place to sit and eat something while they waited for Father. He stares in wonder as she does it again, noticing how little ice-cream she actually puts on the spoon that she sucks on deeply, this was going to take a while, and his dick was already hard. He felt it throbbing against his pant wanting to be released, he watches the spoon disappear again, like a magic trick. He reaches down in an attempt to cover himself, laying his hand gently over the bulge in his pants. He soon moves it away, when he realises that he is rubbing himself, that's only going to make it worse.

"What are you doing?" He questions, slightly harsher than he meant.

"Eating ice-cream." She answers sweetly, a small smile stretches across her beautiful lips, eyelashes fluttering and she continues 'eating' with a smile. He looks down at his own ice-cream and picks up the tiny spoon, he stares at it for a moment, his dick twitches again just by looking at it and visualising what he would see if he were to look up a few centimetres. He started on his ice-cream, refusing to look up, no-one has ever had this much power over him, certainly not a girl.

"Isn't it delicious?" She inquiries, he glances up to see a large grin across her, and he feels his own lips twitch up at the corners when he hears her giggle. She knew exactly what she was doing. He quickly stands up grabbing her arm and dragging her out the back, he slams her against the wall. He stares at her for a moment before their mouths slam together: His mouth hard on hers, unyielding; he feels her responding, so he places both arms around her and pulled her tight against him. His lips soften slightly enjoying the feel of her lips against his. He reaches up and tugs on her hair, winding his fingers through her curls. He was appreciating the feeling of her heart hammer against his chest when the door opens behind him. He turns and punches the skinny mundane hard, vaguely hearing Clary scream, and a tugging on his arm.

"SIMON!" Clary exclaims, jumping in front of him.

"Clary, what are you doing here, I figured you weren't allowed to leave home." The weakling responds, Clary leans down and hugs him tightly. Jonathan crosses his arms across his chest and stares at his sister, silently warning her not to say something she will regret.

"Technically, I wasn't, I might have broken out…" She replies somewhat truthfully, releasing herself from the mundane's grip. Jonathan stares at the weakling, question why she felt the need to be around him. Simon turns to him and stares at him for a moment, before turning back to Clary,

"Who's your friend?" He asks, looking back to Jonathan who scowls in response.

"Jonathan? He's not really my friend…" Clary replies, looking at Jonathan. Who veins shock horror, placing his hand over his heart, attempting to look hurt, he wanted to be much more than a friend anyway, and he knew she did also. "He just wanted to buy me some ice-cream." Clary elaborates, in response to Simon's raised eyebrows.

"Well, in that case, you can come to Eric's poetry, it's just around the corner from here," He inquiries, looking sickeningly, hopeful to spend time with his sister. Jonathan tries to catch Clary's gaze.

"No… I would really rather not, I got a headache last time." Clary replies, rubbing her temples as if to prove a point. Father was going to be here any second and he wanted as much time alone with her as possible. "But you should still go, he's your friend-" Clary tries to reason, but is rudely interrupted.

"So are you." He argued looking hurt, Jonathan smirks, and walk up to Clary, tugging her to his chest. Gaining him an evil look from mundane.

"It's fine, I need to get back home soon anyway." She explained trying to stifle the blow.

"Fine." He replied angrily, turning and also giving him an evil look as he walks away. He smiled sweetly at the idiot as he leaves. He follows the mundane with his eyes until he was out of sight.

* * *

"Well, that was awkward…" Clary exclaims, feeling horrible, she had never seen Simon so hurt. Today was officially the worst day of her life, and it wasn't even over yet. She turned back to Jonathan, releasing a breath she didn't realise she was holding… at least there's was one good thing that has come out of today… she thought as she looked into his smouldering, black orbs. His eyebrows furrow as he looks over her shoulder.

"Come." He orders simply, grabbing her arm and dragging her out of the shop before she could respond.

"Wait… Jonathan… Where are we going?" She questions while being pulled along quickly.

"Shhh, be quiet and look apologetic, he's not going to be happy that you tried to run away." He replies as he drags her into an alley. She sees Valentine, her Father, standing there arms crossed across his chest, black eyes glaring at her angrily.

"Clarissa, my dear, I am glad to see you are safe, but I regret to inform you, that you are grounded for a week." He declares before sighing and rubbing his temple. "I can't have my daughter running away every time she feels threatened. If you have a problem, you face it and deal with it. You are a Morgenstern you do not run from your problems." She does as Jonathan suggest and stays quiet, looking down, attempting to look apologetic. He sighs again, looking around to avoid looking at her.

"Jonathan, take her home. I still have some work to do here. I will be seeing you both for dinner at seven o'clock, sharp, do not be late." He warns staring intently at her. Clary feels Jonathan nod at her side, before dragging her through a wall that was once solid.


End file.
